The Victims Commissioner and nationalist politicians have accused the Northern Ireland Secretary of displaying insensitivity and offending victims of the conflict.
Theresa Villiers suggested most people did not wake up worrying about the past and called for "proportionate" focus on wrongdoing by republicans and loyalists rather than the police as part of future measures to heal divisions.
Commissioner Kathryn Stone cautioned politicians against adopting a simplistic view as she announced she is to take up a post in England.
And senior Sinn Fein member Gerry Kelly claimed the Government had positioned itself firmly on unionist ground.
He added: "Theresa Villiers's claims that there has been too much focus on state killings stems from the fact that during the conflict state killings and collusion were never properly investigated.
"And the reason so many cases on state killings are now going through the courts is that families are being denied the truth about the murder of their loved ones right up until the present day."
Ms Villiers gave a keynote speech in Belfast and said the vast majority of people in Northern Ireland did not wake up on a Monday morning worrying about the past, flag flying or contentious parades.
Ms Stone claimed Ms Villiers's comments were: "Insensitive to thousands of victims and survivors who do wake up every morning living with the legacy of the past and fearing what new trauma is around the corner.
"Victims and survivors have given politicians a brave, dignified and progressive lead on what we need to do to address the very real and difficult issue of dealing with the past."
Victims on both sides have demanded justice for the loss of loved ones while human rights lawyers have argued that truth recovery is vital to help heal deep wounds which still exist in Northern Ireland society.
Five-party political talks broke down before the new year on dealing with controversial parades through neighbourhoods where they are not welcome, the catalyst for serious street violence every summer.
Other issues on the agenda included the flying of Union flags from official buildings and establishing structures to address the past and victims' needs.
Democratic Unionist Party deputy leader Nigel Dodds said there had been a disproportionate focus on the past actions of the state and an almost total lack of consideration given to innocent victims of deaths caused by paramilitaries.
"The facts are clear - 90% of deaths in Northern Ireland were caused by paramilitaries, and of those, two-thirds were by republicans.
"The IRA killed more Catholics than either the RUC or the Army, yet there has been a concentration of resources and calls for inquiries on a very small number of deaths."
Ms Villiers argued that any processes for addressing the legacy of the past - during which thousands were killed or maimed amid 30 years of bombings and shootings - have almost exclusively concentrated on the activities of security forces, rather than paramilitaries who were responsible for most cases.
The devolved ministerial Executive at Stormont is spending more than £30 million a year on historical matters, with police trawling hundreds of thousands of documents, in part to investigate shootings carried out by former officers or soldiers.
Ms Villiers said: "At least with a new process, agreed by Northern Ireland's political leaders, there is scope to write in from the start the need for an objective balance and with proper weight and a proportionate focus on the wrongdoing of paramilitaries ... rather than the almost exclusive concentration on the activities of the state which characterises so many of the processes currently under way."
Dozens of inquests are probing Troubles killings while civil High Court cases are being taken in Belfast by victims alleging state collusion in murder.
The Police Service of Northern Ireland (PSNI) has reopened some criminal investigations, has a dedicated team of detectives to probe old cases dating back to before the start of the conflict in 1968 for fresh leads and has to decide whether it is safe to disclose old records during myriad inquests.
While many unionists venerate former soldiers and members of the Royal Ulster Constabulary for holding the line against republican terrorists, some nationalists accuse state forces of adopting a shoot to kill policy, co-operating with loyalist terror gangs and ensuring people needlessly lost their lives.
Nationalist SDLP Stormont assembly member Alex Attwood said any process on the past, if it is to be ethical, must be comprehensive.
He added: "What the state did must be accounted for and what the terror groups did must be accounted for; otherwise victims and survivors will again be badly let down. For that to be credible, the process must be balanced."